Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
what's difference between a read marked by "sam FLAG 1024" and marked by " PG:markduplicates" ?
1 . when I run the following command : "samtools view -h -f 1024 bwa.raw.bam " , then can not get any reads , so I think BWA do not markduplicates to use" FLAG 1024". 2 after I deal with bwa.raw.bam with using picard-markduplicates , "samtools view -h -f 1024 baw.raw.markdup.bam " , I got some reads with the below marks : FLAG : 1187 PG:Z:MarkDuplicates SO i got a question : I know the option "-f 1024" is just for optical or pcr dups , but I do not know which software modify "FLAG" to add "1024" ?? according to 1 , I think BWA do not do that becasue no reads found . however ,according to 2 , I got reads markd by "FLAG 1024", so I guess when I do the picard-markduplicates step , picard will modify sam flag ?? ,not just add "PG:Z:MarkDuplicates" .